Structure of PDB 6mtd Chain v Binding Site BS04

Receptor Information

>6mtd Chain v (length=839) Species: 9986 (Oryctolagus cuniculus)

VNFTVDQIRAIMDKKANIRNMSVIAHVDHGKSTLTDSLVCKAGIIARCIT
IKSTAISLFYELSENDLNFIKQSKDGAGFLINLIDSPGHVDFSSEVTAAL
RVTDGALVVVDCVSGVCVQTETVLRQAIAERIKPVLMMNKMDRALLELQL
EPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFGSGLH
GWAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPA
NGKFSKSATSPEGKKLPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKL
DIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMITIHLPSPVTAQKYRC
ELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSG
LVSTGLKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNI
VGLVGVDQFLVKTGTITTFEHAHNMRVMKFSVSPVVRVAVEAKNPADLPK
LVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLEEDHACIP
IKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMKARPFPDGLAEDIDK
GEVSARQELKQRARYLAEKYEWDVAEARKIWCFGPDGTGPNILTDITKGV
QYLNEIKDSVVAGFQWATKEGALCEENMRGVRFDVHDVTLHADAIHRGGG
QIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGH
VFEESQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQI
LPGDPFDNSSRPSQVVAETRKRKGLKEGIPALDNFLDKL

Ligand information

• Ligand ID: GDP
• InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 6mtd Chain v Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6mtd Structures of translationally inactive mammalian ribosomes.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): V28 D29 G31 K32 S33 T34 K159 D161 S216 L218
• Binding residue (residue number reindexed from 1): V27 D28 G30 K31 S32 T33 K140 D142 S197 L199
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sat Nov 16 16:33:59 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()

   1435     title=pdb2title(pdbid)

   1436     if bs.startswith("BS"):

=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)

   1438     else:

   1439         if lig3:

pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '6mtd', asym_id = 'v', bs = 'BS04', title = 'Structures of translationally inactive mammalian ribosomes.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6mtd', asym_id='v', bs='BS04', title='Structures of translationally inactive mammalian ribosomes.')

   1295         display_ec(ec,csaOrig,csaRenu)

   1296     if go:

=> 1297         display_go(go,uniprot,pdbid,asym_id)

   1298     return pubmed,uniprot

   1299 

global display_go = <function display_go>, go = '0003924,0005525', uniprot = '', pdbid = '6mtd', asym_id = 'v'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003924,0005525', uniprot='', pdbid='6mtd', asym_id='v')

    480         '''.replace("$namespace_link",namespace_link

    481           ).replace("$namespace",namespace

=>  482           ).replace("$uniprot",u

    483         ))

    484         for l,(term,name) in enumerate(go2aspect[Aspect]):

u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>